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Author SHA1 Message Date
Edmund Miller
8cd635f757
ci(fastqc): Fix test matrix 2020-12-01 11:13:43 -06:00
Abhinav Sharma
4e657c82e2 Move the MultiQC test files to data folder 2020-12-01 12:27:31 +05:30
Abhinav Sharma
b43c1f3937 Refactor the multiqc test code 2020-12-01 12:19:52 +05:30
Abhinav Sharma
131609dc05 Tweak the output section to make the tests pass 2020-12-01 12:03:37 +05:30
Paolo Cozzi
835ac48565 Fixing MULTIQC module and adding tests (#1) 
* fix multiqc process

* fix multiqc tests

* move multiqc test input data into tests/data/fastqc/ folder

Move input tests data into tests/data/fastqc/ and linking those files into software/multiqc/test/input/ as stated from the project documentation

* add multiqc github workflow

* remove unused file

* generalize multiqc input data

User must collect all desidered files in a channel (as described in https://seqera.io/training/#_multiqc_report

* update meta information
 2020-12-01 12:03:37 +05:30
Abhinav Sharma
2783913122 initial attempt for multiqc module 2020-12-01 12:03:37 +05:30
Edmund Miller
98c629583a
ci: Test whether subdirectories are breaking workflows 2020-11-30 19:03:56 -06:00
Edmund Miller
7d2b74a5f7
ci(fastqc): Use a test matrix for NXF versions 2020-11-30 18:57:56 -06:00
Harshil Patel
e02f0de514
Merge pull request #87 from drpatelh/rsem_index 
Use STAR to build initial index for RSEM
 2020-11-30 14:45:32 +00:00
drpatelh
e5c7ecc89c Use STAR to build initial index for RSEM 2020-11-30 11:29:24 +00:00
Edmund Miller
036427d73c
ci(pytest-workflow): Fix trigger paths 2020-11-24 21:24:55 -06:00
Edmund Miller
6eeb930bdb
chore: Remove test directory from dummy tool 2020-11-24 21:09:55 -06:00
Edmund Miller
86219a586b
ci(trimgalore): Use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
2fc39e02e2
test(trimgalore): Refactor se and pe to use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
445498d0c3
ci(samtools): Run tests with pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
b2cd464ad3
test(samtools): Refactor stats to use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
36bbf6baa3
test(samtools): Refactor sort to use pytest-workflow 
Pretty sure this is passing it a sorted bam though?
 2020-11-24 21:08:34 -06:00
Edmund Miller
6448638b55
test(samtools): Refactor index to use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
16cb794892
test(samtools): Refactor idxstats to use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
34d86427a6
test(samtools): Refactor flagstat to use pytest-workflow 2020-11-24 21:08:33 -06:00
Edmund Miller
ebf3a4529f
ci(picard): Update markduplicates 2020-11-24 21:08:33 -06:00
Edmund Miller
d1a77b2fb2
test(picard): Add failing test for markduplicates 2020-11-24 21:08:33 -06:00
Edmund Miller
7848019cdb
test(picard): Refactor markduplicates to use pytest-workflow 2020-11-24 21:08:33 -06:00
Edmund Miller
d009420a0c
test(fastqc): Fix md5sums 
These must have gotten messed up at some point
83539fcdf2 is my guess
 2020-11-24 21:08:33 -06:00
Edmund Miller
939f5ca744
test(picard): Refactor collectmultiplemetrics to use pytest-workflow 2020-11-24 21:03:40 -06:00
Edmund Miller
234e85bdce
test(picard): Refactor mergesamfiles to use pytest-workflow 2020-11-24 19:01:12 -06:00
Edmund Miller
016d8684f3
test(bwa): Refactor to use pytest-workflow 2020-11-24 19:00:11 -06:00
Edmund Miller
dfc8528df9
ci: Remove docker workflow 
This only applies to deprecated software
 2020-11-24 18:58:02 -06:00
Edmund Miller
691df9d469
style(actions): Create seperate software dir 
For future subworkflows
 2020-11-24 18:57:53 -06:00
Harshil Patel
794a5cbd0c
Merge pull request #80 from nf-core/pytest-workflow 
Pytest-workflow
 2020-11-24 22:55:07 +00:00
Edmund Miller
83539fcdf2
test(fastqc): restructure under software/fastqc 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-11-24 15:30:51 -06:00
Edmund Miller
b96f2d6a5e test(config): One config to rule them all 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-11-24 20:26:04 +00:00
Edmund Miller
2e56022e31 test(fastqc): Remove input symlinks 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-11-24 20:26:04 +00:00
Edmund Miller
1fd97e8804 test(fastqc): Fix md5sums 2020-11-24 20:26:04 +00:00
Edmund Miller
ba681c6f27 refactor(pytest-workflow): Move fastqc tests to tests/ 2020-11-24 20:26:04 +00:00
Edmund Miller
f235732a58
ci(fastqc): Use both threads in GitHub runner 2020-11-16 13:45:00 -06:00
Edmund Miller
c264c66a49
test(fastqc): Use -entry to speed up tests 
`--wt, --workflow-threads` is now an option and can be used to run tests
simultaneously.
 2020-11-16 13:41:59 -06:00
Edmund Miller
a4544a11ad
chore(fastqc): Remove test output 2020-11-16 10:22:19 -06:00
Edmund Miller
29937fe198
test(fastqc): Add expected files and md5sums 
The md5 sums change for the zip files every run so it's difficult to hit
a moving target.
 2020-11-16 10:20:29 -06:00
Edmund Miller
6d857a2584
ci(fastqc): Run pytest-workflow instead of workflow 
This will check for the actual output files and their contents not just
whether the module runs or not.
 2020-11-16 09:37:45 -06:00
Edmund Miller
07017f401e
test(fastqc): Add initial pytest-workflow 2020-11-16 09:35:01 -06:00
Harshil Patel
751204ef33
Merge pull request #76 from drpatelh/versions 
Remove Singularity image path
 2020-11-12 15:27:06 +00:00
drpatelh
082c582258 Remove EClint for now 2020-11-12 15:22:15 +00:00
drpatelh
a3f46865ff Remove Singularity image path 2020-11-12 14:55:16 +00:00
Harshil Patel
65ba3128ee
Merge pull request #72 from drpatelh/versions 
Update badges in README
 2020-10-20 11:09:50 +01:00
drpatelh
99f5d49d37 Update README 2020-10-20 11:04:12 +01:00
drpatelh
5eb735f561 Update README 2020-10-20 11:02:46 +01:00
Harshil Patel
86dca6bfc2
Merge pull request #71 from drpatelh/versions 
Update picard version command and default container
 2020-10-20 10:24:02 +01:00
drpatelh
47d390772c Update picard version command and default container 2020-10-19 15:17:19 +01:00
Harshil Patel
ff0fe1a910
Merge pull request #70 from drpatelh/versions 
Update existing modules with new options and container syntax
 2020-10-15 11:28:13 +01:00